Linkage disequilibrium and haplotypes of five TP53 polymorphisms in oesophageal cancer patients

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Date
2020-07
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Indian Academy of Sciences
Abstract
The aim of present study was to evaluate the linkage disequilibrium (LD) of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[a polymorphism of TP53 and their haplotypes association with oesophageal cancer risk in patients from Punjab, northwest India. A total of 466 samples, including 233 oesophageal cancer patients and 233 healthy individuals were analysed. Data analysis revealed the gender specific association. In female group, arginine–proline (RP) genotype (P = 0.08) and P allele (P = 0.07) of p.R72P polymorphism was marginally associated with increased risk of oesophageal cancer. A1A2 genotype (P = 0.06) and A2 allele (P = 0.07) of PIN3 Ins16bp polymorphism was marginally associated with decreased risk of oesophageal cancer in male group. A1A2–GA genotype combination (P = 0.04) of PIN3 and r.13494g[a polymorphisms was significantly associated with decreased risk of oesophageal cancer in male group. In female group, PP–GA genotype combination (P = 0.02) of p.R72P and r.13494g[a polymorphisms and RP–A1A1–GG genotype combination (P = 0.04) of p.R72P, PIN3 and r.13494g[a polymorphisms was significantly associated with increased risk of oesophageal cancer. We observed moderate LD between two intronic polymorphisms PIN3 Ins16bp and r.13494g[a (D0 = 0.90; r 2 = 0.68). Haplotype analysis revealed that none of the haplotype combination was associated with oesophageal cancer risk when both the genders were considered. Stratification on the basis of gender showed that P-A2-P-A-A haplotype of p.R72P, PIN3 Ins16bp, p.P47S, p.R213R and r.13494g[a polymorphisms was marginally associated with reduced oesophageal cancer risk in male group (P = 0.08). Replication of these findings in independent cohorts may be insightful for the role of TP53 in oesophageal cancer pathogenesis.
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Keywords
oesophageal cancer, TP53 polymorphism, polymorphism, haplotype, linkage disequilibrium
Citation
Sambyal Vasudha, Kaur Sukhpreet, Manjari Mridu, Uppal Manjit Singh, Singh Neeti Rajan, Sudan Meena, Guleria Kamlesh. Linkage disequilibrium and haplotypes of five TP53 polymorphisms in oesophageal cancer patients. Journal of Genetics. 2020 Jul; 99: 1-10
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https://imsear.searo.who.int/handle/123456789/215498
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Journal of Genetics